Cell-based studies yield data averaged over a large number of cells which overlook the rich information that can possibly be obtained when cells are studied individually. For this reason, much emphasis has been placed over the past decades to develop single-cell microarray to study each cell individually.However, the current techniques for generating single-cell microarray by using electromagnetic forces needs special medium and may have unknown effects, whereas mechanical methods are unable to trap cells with different sizes and are slow. Efficiency is also a concern for current techniques.Here, we demonstrate for the first time an anti-clogging 3D porous film that is integrated in a micro-filter device for patterning of single-cells in microarray format. An interesting feature of this 3D membrane is that cells of different sizes can be trapped which is important for trapping single-cells (cells have inhomogeneous size-distribution. A new method has been developed here to fabricate 3D micro-structures integrated film.The porous film integrated with 3D microstructures has been successfully fabricated and high density single-cell microarray has been generated by using the 3D porous membrane with efficiency close to 90% (Fig.3a). The cell-viability of more than 90% has been achieved in this device.